Search for: All records

A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergentcis-regulatory sequences. It remains unclear how such drasticcis-regulatory evolution across species allows preservation of gene function, and to what extent these differences influence howcis-regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ~125 million years. Usingin-vivogenome editing in two distantly related models,Arabidopsis thaliana(Arabidopsis) andSolanum lycopersicum(tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor geneCLAVATA3(CLV3) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomatoCLV3are highly sensitive to even small perturbations compared to its downstream region. In contrast, ArabidopsisCLV3function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of ArabidopsisCLV3caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functionalcis-regulatory sequences. Our results demonstrate remarkable malleability incis-regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration ofcis-regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture ofcis-regulation to effectively engineer trait variation from conserved productivity genes in crops. 

Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for predicting many complex traits. However, it usually cannot capture the combination of alleles in haplotypes and it has generated little insight about the biological function of polymorphisms. Here we present a novel and cost-effective method for imputingcishaplotype associated RNA expression (HARE), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linkedcisacting causal variants in the immediate vicinity of the gene, while excludingtranseffects from diffusion and metabolism. Therefore, HARE estimates were more transferrable across different tissues and populations compared to measured transcript expression. We also showed that HARE estimates captured one-third of the variation in gene expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels–a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel)–for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues, whereas accuracy by HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations. 

The plastochron, the time interval between the formation of two successive leaves, is an important determinant of plant architecture. We genetically and phenotypically investigated many-noded dwarf ( mnd ) mutants in barley. The mnd mutants exhibited a shortened plastochron and a decreased leaf blade length, and resembled previously reported plastochron1 ( pla1 ), pla2 , and pla3 mutants in rice. In addition, the maturation of mnd leaves was accelerated, similar to pla mutants in rice. Several barley mnd alleles were derived from three genes— MND1 , MND4 , and MND8 . Although MND4 coincided with a cytochrome P450 family gene that is a homolog of rice PLA1 , we clarified that MND1 and MND8 encode an N-acetyltransferase-like protein and a MATE transporter-family protein, which are respectively orthologs of rice GW6a and maize BIGE1 and unrelated to PLA2 or PLA3 . Expression analyses of the three MND genes revealed that MND1 and MND4 were expressed in limited regions of the shoot apical meristem and leaf primordia, but MND8 did not exhibit a specific expression pattern around the shoot apex. In addition, the expression levels of the three genes were interdependent among the various mutant backgrounds. Genetic analyses using the double mutants mnd4mnd8 and mnd1mnd8 indicated that MND1 and MND4 regulate the plastochron independently of MND8 , suggesting that the plastochron in barley is controlled by multiple genetic pathways involving MND1 , MND4 , and MND8 . Correlation analysis between leaf number and leaf blade length indicated that both traits exhibited a strong negative association among different genetic backgrounds but not in the same genetic background. We propose that MND genes function in the regulation of the plastochron and leaf growth and revealed conserved and diverse aspects of plastochron regulation via comparative analysis of barley and rice.